Java Resources for Working with Bioassay Dose Response Curves

A good introduction to useful laboratory and data handling practices for bioassays and HTS can be found in the manual provided by the NIH Chemical Genomic Center. Assay Guidance Manual Version 5.0, 2008, Eli Lilly and Company and NIH Chemical Genomics Center. Also see the Assay Operations for SAR Support for a discussion on DETERMINATION OF EC50/IC50 and Models and Curve Fitting Guidelines Resources for handling Bioassay Data Fitting, QC, Validation and Graphing I've performed searches on this topic at several occasions and I will be adding more references as I find them. Java Resources NIH Chemical Genomics Center CurveFit. The author describes this as a large scale dose response curve fitting and curve classification software. The Java WebStart application is easy to run and gives a good idea of the functions that the software can perform. Experience Downloaded the sample data from the web site for use in testing. The sample data format is somewhat unusual and redundant. It interleaves concentration information (redundant) with compound structures and recorded responses at each concentration. Initially, I had an issue with loading data until I've used the File->Reset Database option. After that I was able to load the sample data and fit the curves. The zip file contains the Java source code. However, there is no documentation and the majority of the source code is without any comments. The library also has other dependencies including a dependency on the commercial Marvin library from chemaxon.com. It's unlikely that this code will be very useful for re-use by others until additional documentation is provided. This is unfortunate, as the availability of an open-source dose response curve fitting library is of unquestionable importance. Michael Thomas Flanagan's Java Scientific Library This is an extensive Java library with many scientific applications. The author has developed this library for teaching purposes and he is also making it freely available for non-commercial purposes. For HTS and bioassay data analysis, I'm interested in the Fit to a Sigmoid Function capability of the Regression class. At this point however, I have no hands on experience with using this library.

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